Moni

Your instincts on the fly paper were pretty good. Yes, the larvae live in the soil and disrupt the roots of the plants. But if you catch most of them on the paper, you stop the whole process on the adult end. No adults, no larvae. Yellow stickie traps sold as white fly traps work even better.
The larvae live in the top 1 inch of soil, so removing that and replacing it with new soil will also help.
And....let the soil dry out a bit. They LOVE moist soil. It is their reason for being.
As for nuking them (I'm grinning now), there are some things you can do. Pyrethrums work pretty well on the adults, as do insecticidal soaps. If you want to nuke the larvae, I would turn to BT (bacillus thuringiensis) that is made specifically for fungus gnat larvae. There are 3 different kinds of BT that deal with different insects. You need to get BT israelensis and water the solution into the soil.
There also are some nematodes that have been used quite successfully on fungus gnat larvae but I am not yet informed enough on them to give advice on their use.
Moni